Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/3810d554b45163ff7b746917800a13/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_5W-N1-BDNA-1_A23H3W5LT3_1/1136_5W-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/3810d554b45163ff7b746917800a13/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_5W-N1-BDNA-1_A23H3W5LT3_1/1136_5W-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_5W-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5W-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5W-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5W-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 72536596 total, 65057 skipped (flags/unmapped)
Fragments: 36405766 total (36033145 tlen-paired, 8828 hash-paired, 4880 singletons, 8182 discordant, 350731 orphans, 7809 too large [>5000 bp], 7119142 duplicates)
Reads: 80021236 total, 59224 skipped (flags/unmapped)
Fragments: 40172938 total (39741268 tlen-paired, 9527 hash-paired, 5162 singletons, 8319 discordant, 408662 orphans, 14980 too large [>5000 bp], 7808784 duplicates)
Reads: 79180948 total, 55235 skipped (flags/unmapped)
Fragments: 39753196 total (39342655 tlen-paired, 8557 hash-paired, 5205 singletons, 5745 discordant, 391034 orphans, 7780 too large [>5000 bp], 7778929 duplicates)
Reads: 81914438 total, 103490 skipped (flags/unmapped)
Fragments: 41313313 total (40046595 tlen-paired, 9783 hash-paired, 5380 singletons, 244143 discordant, 1007412 orphans, 98557 too large [>5000 bp], 7964747 duplicates)